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Isolation of 1,796 SSR clones from SSR-enriched DNA libraries of bunching onion (Allium fistulosum)

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Abstract

Bunching onion (Allium fistulosum L.) is one of the most important vegetables in Japan. To establish a genetic basis for molecular breeding of bunching onion, we isolated 1,796 simple sequence repeat (SSR) clones by large-scale sequencing of SSR-enriched genomic DNA libraries. Of these, 1,331 (74.1%) contained (GT) n repeats (n > 5), while 314 (17.5%) were (GA) n -containing clones. The average number of SSR repeats was 10.5 and 10.4 in the (GT) n - and (GA) n -containing clones, respectively. In a sample of five bunching onion inbred lines, an average of 3.2 alleles were detected in the 100 SSR loci investigated, with the polymorphic information content averaging 0.55. These results indicate that bunching onion SSRs are very rich sources of highly informative genetic markers.

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Abbreviations

EST:

(Expressed sequence tag)

PIC:

(Polymorphic information content)

SSR:

(Simple sequence repeat)

References

  • Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186

    CAS  PubMed  Google Scholar 

  • Bradeen JM, Havey MJ (1995) Randomly amplified polymorphic DNA in bulb onion and its use to assess inbred integrity. J Am Soc Hort Sci 120:752–758

    CAS  Google Scholar 

  • Bredemeijer GMM, Arens P, Wouters D, Visser D, Vosman B (1998) The use of semi-automated fluorescent microsatellite analysis for tomato cultivar identification. Theor Appl Genet 97:584–590

    Article  CAS  Google Scholar 

  • Crockett PA, Bhalla PL, Lee CK, Singh MB (2000) RAPD analysis of seed purity in a commercial hybrid cabbage (Brassica oleracea var. capitata) cultivar. Genome 43:317–321

    Article  PubMed  CAS  Google Scholar 

  • Fischer D, Bachmann K (2000) Onion microsatellites for germplasm analysis and their use in assessing intra- and interspecific relatedness within the subgenus Rhizirideum. Theor Appl Genet 101:153–164

    Article  CAS  Google Scholar 

  • Ford-Lloyd BV, Armstrong SJ (1993) Welsh onion Allium fistulosum L. In: Kalloo G, Bergh BO (eds) Genetic improvement of vegetable crops. Pergamon Press, London, pp 51–58

    Google Scholar 

  • Fukuoka H, Nunome T, Minamiyama Y, Kono I, Namiki N, Kojima A (2005) Read2Marker: a data processing tool for microsatellite marker development from a large data set. BioTechniques 39:472–476

    Article  PubMed  CAS  Google Scholar 

  • Ipek M, Ipek A, Almquist SG, Simon PW (2005) Demonstration of linkage and development of the first low-density genetic map of garlic, based on AFLP markers. Theor Appl Genet 110:228–236

    Article  PubMed  CAS  Google Scholar 

  • Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, van de Wiel C, Bredemeijer G, Vosman B, Matthes M, Daly A, Brettschneider R, Bettini R, Buiatti M, Maestri E, Malcevschi A, Marmiroli N, Aert R, Volckaert G, Rueda J, Linacero R, Vazquez A, Karp A (1997) Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Mol Breed 3:381–390

    Article  CAS  Google Scholar 

  • King JJ, Bradeen JM, Bark O, McCallum JA, Havey MJ (1998) A low-density map of onion reveals a role for tandem duplication in the evolution of an extremely large diploid genome. Theor Appl Genet 96:52–62

    Article  CAS  Google Scholar 

  • Kirk JTO, Rees H, Evans G (1970) Base composition of nuclear DNA within the genus Allium. Heredity 25:507–512

    CAS  Google Scholar 

  • Kuhl JC, Cheung F, Yuan Q, Martin W, Zewdie Y, MaCallum J, Catanach A, Rutherford P, Sink KC, Jenderk M, Prince JP, Town CD, Havey MJ (2004) A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales. Plant Cell 16:114–125

    Article  PubMed  Google Scholar 

  • Kumazawa S, Katsumata H (1965) Negi (Japanese bunching onion). In: Kumazawa S (ed) Sosai-engei kakuron (Vegetable crops). Yokendo Press, Tokyo, pp 280–289, (In Japanese)

    Google Scholar 

  • Lagercrantz U, Ellegren H, Andersson L (1993) The aboundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acid Res 21:1111–1115

    Article  PubMed  CAS  Google Scholar 

  • MAFF (2005) Shuyou Nousanbutsu no Sanshutsugaku to Kouseihi (The production of vegetables in Japan). In: MAFF (ed) Seisan Nougyo Shotoku Toukei. (In Japanese). http://www.tdb.maff.go.jp/toukei/a02stoukeiexl?Fname=E015–16–194.xls&PAGE=3&TokID=E015&TokKbn=B&TokID1=E015B2004–002&TokID2=E015B2004–002-004&TokID3=E015B2004-002-004-002. Cited 20 Dec 2006

  • Martin WJ, McCallum J, Shigyo M, Jakse J, Kuhl JC, Yamane N, Pither-Joyce M, Gökçe AF, Sink KC, Town CD, Havey MJ (2005) Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity. Mol Gen Genomics 274:197–204

    Article  CAS  Google Scholar 

  • Nunome T, Negoro S, Miyatake K, Yamaguchi H, Fukuoka H (2007) A protocol for the construction of microsatellite enriched genomic library. Plant Mol Biol Rep (in press)

  • Ohara T, Song YS, Tsukazaki H, Wako T, Nunome T, Kojima A (2005) Construction of a genetic linkage map of Japanese bunching onion (Allium fistulosum) based on AFLP and SSR markers. Euphytica 144:255–263

    Article  CAS  Google Scholar 

  • Ricroch A, Yockteng R, Brown SC, Nadot S (2005) Evolution of genome size across some cultivated Allium species. Genome 48:511–520

    Article  PubMed  CAS  Google Scholar 

  • Song YS, Suwabe K, Wako T, Ohara T, Nunome T, Kojima A (2004) Development of microsatellite markers in bunching onion (Allium fistulosum L.). Breed Sci 54:361–365

    Article  CAS  Google Scholar 

  • Stack SM, Coming DE (1979) The chromosomes an DNA of Allium cepa. Chromosoma 70:161–181

    Article  CAS  Google Scholar 

  • van Heusden AW, van Ooijen JW, Vrielink-van Ginkel R, Verbeek WHK, Wietsma WA, Kik C (2000) A genetic map of an interspecific cross Allium based on amplified fragment length polymorphism (AFLP) markers. Theor Appl Genet 100:118–126

    Article  Google Scholar 

  • Wako T, Ohara T, Song YS, Kojima A (2002) Development of SSR markers in bunching onion. Breed Res 4(Suppl. 1):83 (In Japanese)

    Google Scholar 

  • Wilkie SE, Isaac PG, Slater RJ (1993) Random amplified polymorphic DNA (RAPD) markers for genetic analysis in Allium. Theor Appl Genet 86:497–504

    Article  CAS  Google Scholar 

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Acknowledgements

We are grateful to Ms. K. Tanaka and Ms. K. Wakita for their skillful technical assistance in DNA extraction and PCR amplification. This work was supported by the project “Green Technology Project (DM-1604)”, Ministry of Agriculture, Forestry and Fisheries, Japan.

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Authors and Affiliations

  1. National Institute of Vegetable and Tea Science (NIVTS), NARO, 360 Ano-Kusawa, Tsu, Mie, 514-2392, Japan

    Hikaru Tsukazaki, Tsukasa Nunome, Hiroyuki Fukuoka, Ken-ichiro Yamashita, Tadayuki Wako & Akio Kojima

  2. Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF), 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki, 305-0854, Japan

    Hiroyuki Kanamori & Izumi Kono

Authors
  1. Hikaru Tsukazaki
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  2. Tsukasa Nunome
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  3. Hiroyuki Fukuoka
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  4. Hiroyuki Kanamori
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  5. Izumi Kono
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  6. Ken-ichiro Yamashita
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  7. Tadayuki Wako
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  8. Akio Kojima
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Correspondence to Hikaru Tsukazaki.

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Tsukazaki, H., Nunome, T., Fukuoka, H. et al. Isolation of 1,796 SSR clones from SSR-enriched DNA libraries of bunching onion (Allium fistulosum). Euphytica 157, 83–94 (2007). https://doi.org/10.1007/s10681-007-9398-2

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  • DOI: https://doi.org/10.1007/s10681-007-9398-2

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